Magnesium in PDB 1khz: Structure of the Adpr-Ase in Complex with Ampcpr and Mg
Enzymatic activity of Structure of the Adpr-Ase in Complex with Ampcpr and Mg
All present enzymatic activity of Structure of the Adpr-Ase in Complex with Ampcpr and Mg:
3.6.1.13;
Protein crystallography data
The structure of Structure of the Adpr-Ase in Complex with Ampcpr and Mg, PDB code: 1khz
was solved by
S.B.Gabelli,
M.A.Bianchet,
M.J.Bessman,
L.M.Amzel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
26.64 /
2.04
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.100,
67.400,
96.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
25.7
|
Other elements in 1khz:
The structure of Structure of the Adpr-Ase in Complex with Ampcpr and Mg also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg
(pdb code 1khz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Structure of the Adpr-Ase in Complex with Ampcpr and Mg, PDB code: 1khz:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 1khz
Go back to
Magnesium Binding Sites List in 1khz
Magnesium binding site 1 out
of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:19.5
occ:1.00
|
O
|
B:HOH407
|
2.0
|
19.4
|
1.0
|
O
|
B:HOH403
|
2.1
|
17.4
|
1.0
|
OE2
|
B:GLU116
|
2.1
|
19.4
|
1.0
|
O1A
|
B:ADV402
|
2.1
|
17.6
|
1.0
|
OE2
|
B:GLU164
|
2.2
|
22.5
|
1.0
|
OE1
|
B:GLU112
|
2.2
|
17.9
|
1.0
|
CD
|
B:GLU164
|
3.1
|
27.7
|
1.0
|
CD
|
B:GLU116
|
3.2
|
17.8
|
1.0
|
PA
|
B:ADV402
|
3.2
|
18.4
|
1.0
|
CD
|
B:GLU112
|
3.2
|
18.1
|
1.0
|
MG
|
B:MG310
|
3.3
|
19.5
|
1.0
|
OE1
|
B:GLU164
|
3.4
|
26.4
|
1.0
|
O2A
|
B:ADV402
|
3.5
|
17.3
|
1.0
|
MG
|
B:MG304
|
3.5
|
23.4
|
1.0
|
OE2
|
B:GLU112
|
3.6
|
19.6
|
1.0
|
O5'
|
B:ADV402
|
3.6
|
19.2
|
1.0
|
CG
|
B:GLU116
|
3.6
|
16.6
|
1.0
|
O
|
B:HOH409
|
3.6
|
19.3
|
1.0
|
OE1
|
B:GLU162
|
3.8
|
42.1
|
1.0
|
O
|
B:ALA96
|
4.0
|
18.4
|
1.0
|
OE1
|
B:GLU115
|
4.2
|
24.4
|
1.0
|
OE1
|
B:GLU116
|
4.3
|
18.4
|
1.0
|
C5'
|
B:ADV402
|
4.4
|
18.2
|
1.0
|
O
|
B:HOH404
|
4.4
|
17.1
|
1.0
|
CG
|
B:GLU164
|
4.5
|
27.7
|
1.0
|
CG
|
B:GLU112
|
4.6
|
18.7
|
1.0
|
CD
|
B:GLU162
|
4.6
|
42.7
|
1.0
|
CX
|
B:ADV402
|
4.7
|
18.9
|
1.0
|
OE2
|
B:GLU162
|
4.7
|
45.0
|
1.0
|
CA
|
B:GLY97
|
4.7
|
15.5
|
1.0
|
O
|
B:HOH405
|
4.7
|
23.5
|
1.0
|
O
|
B:HOH410
|
4.8
|
16.1
|
1.0
|
CB
|
B:GLU112
|
4.9
|
17.4
|
1.0
|
O2B
|
B:ADV402
|
4.9
|
21.3
|
1.0
|
C
|
B:ALA96
|
5.0
|
17.2
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 1khz
Go back to
Magnesium Binding Sites List in 1khz
Magnesium binding site 2 out
of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:23.4
occ:1.00
|
O
|
B:HOH405
|
1.8
|
23.5
|
1.0
|
O
|
B:HOH407
|
2.0
|
19.4
|
1.0
|
O
|
B:HOH404
|
2.2
|
17.1
|
1.0
|
O2A
|
B:ADV402
|
2.2
|
17.3
|
1.0
|
OE2
|
B:GLU112
|
2.2
|
19.6
|
1.0
|
O
|
B:HOH406
|
2.3
|
21.6
|
1.0
|
CD
|
B:GLU112
|
3.2
|
18.1
|
1.0
|
PA
|
B:ADV402
|
3.3
|
18.4
|
1.0
|
OE2
|
B:GLU162
|
3.4
|
45.0
|
1.0
|
MG
|
B:MG301
|
3.5
|
19.5
|
1.0
|
OE1
|
B:GLU112
|
3.5
|
17.9
|
1.0
|
O5'
|
B:ADV402
|
3.6
|
19.2
|
1.0
|
O1A
|
B:ADV402
|
3.7
|
17.6
|
1.0
|
O
|
B:HOH480
|
3.8
|
32.5
|
1.0
|
O
|
B:HOH506
|
4.0
|
35.6
|
1.0
|
NH1
|
B:ARG111
|
4.1
|
24.1
|
1.0
|
OE1
|
B:GLU162
|
4.1
|
42.1
|
1.0
|
CD
|
B:GLU162
|
4.1
|
42.7
|
1.0
|
N
|
B:MET98
|
4.1
|
20.1
|
1.0
|
OE1
|
B:GLU115
|
4.2
|
24.4
|
1.0
|
O
|
B:HOH403
|
4.4
|
17.4
|
1.0
|
CA
|
B:GLY97
|
4.4
|
15.5
|
1.0
|
O
|
B:MET98
|
4.6
|
17.7
|
1.0
|
CG
|
B:GLU112
|
4.6
|
18.7
|
1.0
|
NH2
|
B:ARG111
|
4.7
|
25.0
|
1.0
|
CX
|
B:ADV402
|
4.8
|
18.9
|
1.0
|
C
|
B:GLY97
|
4.8
|
17.4
|
1.0
|
CZ
|
B:ARG111
|
4.9
|
25.4
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 1khz
Go back to
Magnesium Binding Sites List in 1khz
Magnesium binding site 3 out
of 3 in the Structure of the Adpr-Ase in Complex with Ampcpr and Mg
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Adpr-Ase in Complex with Ampcpr and Mg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg310
b:19.5
occ:1.00
|
O
|
B:HOH410
|
2.0
|
16.1
|
1.0
|
O2B
|
B:ADV402
|
2.1
|
21.3
|
1.0
|
O
|
B:ALA96
|
2.2
|
18.4
|
1.0
|
OE2
|
B:GLU116
|
2.2
|
19.4
|
1.0
|
O
|
B:HOH409
|
2.3
|
19.3
|
1.0
|
O1A
|
B:ADV402
|
2.3
|
17.6
|
1.0
|
CD
|
B:GLU116
|
3.1
|
17.8
|
1.0
|
OE1
|
B:GLU116
|
3.2
|
18.4
|
1.0
|
PB
|
B:ADV402
|
3.3
|
20.9
|
1.0
|
MG
|
B:MG301
|
3.3
|
19.5
|
1.0
|
PA
|
B:ADV402
|
3.4
|
18.4
|
1.0
|
C
|
B:ALA96
|
3.4
|
17.2
|
1.0
|
CX
|
B:ADV402
|
3.6
|
18.9
|
1.0
|
OE2
|
B:GLU164
|
3.7
|
22.5
|
1.0
|
NH2
|
B:ARG79
|
3.9
|
21.9
|
1.0
|
O1B
|
B:ADV402
|
3.9
|
20.0
|
1.0
|
OE1
|
B:GLU112
|
4.1
|
17.9
|
1.0
|
O
|
B:HOH425
|
4.3
|
21.2
|
1.0
|
NE2
|
B:GLN77
|
4.3
|
23.3
|
1.0
|
CA
|
B:ALA96
|
4.3
|
17.0
|
1.0
|
O5'
|
B:ADV402
|
4.3
|
19.2
|
1.0
|
N
|
B:ALA96
|
4.3
|
16.1
|
1.0
|
O2A
|
B:ADV402
|
4.4
|
17.3
|
1.0
|
N
|
B:GLY97
|
4.4
|
14.6
|
1.0
|
CA
|
B:GLY97
|
4.5
|
15.5
|
1.0
|
C5'
|
B:ADV402
|
4.5
|
18.2
|
1.0
|
CG
|
B:GLU116
|
4.5
|
16.6
|
1.0
|
CB
|
B:ALA96
|
4.5
|
16.3
|
1.0
|
OR5
|
B:ADV402
|
4.6
|
21.2
|
1.0
|
OE1
|
B:GLN77
|
4.7
|
22.2
|
1.0
|
CR5
|
B:ADV402
|
4.9
|
22.4
|
1.0
|
O
|
B:HOH407
|
4.9
|
19.4
|
1.0
|
CZ
|
B:ARG79
|
4.9
|
20.7
|
1.0
|
CD
|
B:GLU164
|
4.9
|
27.7
|
1.0
|
CD
|
B:GLN77
|
5.0
|
20.9
|
1.0
|
|
Reference:
S.B.Gabelli,
M.A.Bianchet,
Y.Ohnishi,
Y.Ichikawa,
M.J.Bessman,
L.M.Amzel.
Mechanism of the Escherichia Coli Adp-Ribose Pyrophosphatase, A Nudix Hydrolase. Biochemistry V. 41 9279 2002.
ISSN: ISSN 0006-2960
PubMed: 12135348
DOI: 10.1021/BI0259296
Page generated: Tue Aug 13 07:44:13 2024
|